There are many options for the detection and speciation of microsporidia in clinical specimens. Light microscopy allows for detection of the parasites, but does not allow speciation. Electron microscopy is the gold standard for speciation, but is insensitive as a method of detection of microsporidia. The polymerase chain reaction (PCR) is a sensitive technique with many different methods for confirming a positive result and determining the genus and species causing an infection. Speciation can be achieved by using species- specific primers in the PCR assay, or by using DNA probes or restriction endonucleases to determine the species after the PCR assay is performed. Single strand confirmation polymorphism (SSCP) combined with PCR (PCR-SSCP) has been used to identify bacteria, fungi, and viruses. We will use our PCR assay for the detec-tion of microsporidia in stool specimens and apply SSCP to determine the specific genus and species of the parasite. Organisms from cell culture will also be used to validate the method. This portion of the project is near completion and will soon be submitted for publication. The project has been expanded to apply SSCP to the detection of microsporidial genotypes for use in epidemiological studies. Newly published primers allow speciation when the PCR products are digested with restriction enzymes. SSCP analysis will make this task easier and more sensitive than restriction enzyme analysis.